Run ID: ERR4192364
Sample name:
Date: 2024-10-05T13:56:55.080815
Number of reads: 3694125
Percentage reads mapped: 96.07
Median coverage: 70.0
Strain: lineage5.1
Spoligotype:
Drug-resistance: Sensitive
| Lineage | Family | RDs | Frequency |
|---|---|---|---|
| lineage5 | West-Africa 1 | RD711 | 1.0 |
| lineage5.1 | West-Africa 1 | RD711 | 0.85 |
| Drug | Resistance | Supporting mutations | WHO confidence | Comment |
|---|---|---|---|---|
| rifampicin | ||||
| isoniazid | ||||
| ethambutol | ||||
| pyrazinamide | ||||
| streptomycin | ||||
| fluoroquinolones | ||||
| moxifloxacin | ||||
| ofloxacin | ||||
| levofloxacin | ||||
| ciprofloxacin | ||||
| aminoglycosides | ||||
| amikacin | ||||
| capreomycin | ||||
| kanamycin | ||||
| cycloserine | ||||
| ethionamide | ||||
| clofazimine | ||||
| para-aminosalicylic_acid | ||||
| delamanid | ||||
| bedaquiline | ||||
| linezolid |
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
|---|
| Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
|---|---|---|---|---|---|---|
| gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Uncertain significance | |||||
| gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| gyrA | 9566 | c.2265C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
| moxifloxacin | Not assoc w R - Interim | |||||
| Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
| Rv0010c | 13579 | c.-21G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
| fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| clofazimine | Not assoc w R | |||||
| Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
| hadA | 731750 | c.-180G>C | upstream_gene_variant | 0.98 | isoniazid | |
| rpoB | 761431 | p.Ile542Thr | missense_variant | 1.0 | rifampicin | |
| rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
| Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clofazimine | Uncertain significance | |||||
| Rv1258c | 1407273 | p.Asp23Val | missense_variant | 1.0 | streptomycin | Uncertain significance |
| pyrazinamide | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
| rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472571 | n.726G>T | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472581 | n.736A>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472582 | n.737G>T | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472584 | n.739A>T | non_coding_transcript_exon_variant | 0.11 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrs | 1472585 | n.740A>C | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472623 | n.778A>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472767 | n.922G>C | non_coding_transcript_exon_variant | 0.12 | kanamycin | |
| capreomycin | ||||||
| streptomycin | ||||||
| amikacin | ||||||
| rrs | 1472996 | n.1151T>C | non_coding_transcript_exon_variant | 0.13 | kanamycin | Uncertain significance |
| capreomycin | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| amikacin | Uncertain significance | |||||
| rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.11 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476153 | n.2496T>C | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476164 | n.2507A>G | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476165 | n.2508T>G | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Not assoc w R |
| linezolid | Uncertain significance | |||||
| rrl | 1476204 | n.2547C>T | non_coding_transcript_exon_variant | 0.29 | capreomycin | |
| linezolid | ||||||
| rrl | 1476215 | n.2558C>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| rrl | 1476235 | n.2578A>G | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
| linezolid | ||||||
| rrl | 1476245 | n.2588C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
| linezolid | Uncertain significance | |||||
| inhA | 1673338 | c.-864G>A | upstream_gene_variant | 1.0 | isoniazid | |
| ethionamide | ||||||
| tsnR | 1853565 | c.-41G>A | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
| tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
| tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
| bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| ndh | 2101921 | c.1122G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| delamanid | Not assoc w R - Interim | |||||
| ethionamide | Not assoc w R - Interim | |||||
| ndh | 2103112 | c.-70G>T | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R - Interim |
| delamanid | Uncertain significance | |||||
| ethionamide | Uncertain significance | |||||
| katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
| PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
| PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.27 | pyrazinamide | |
| PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.28 | pyrazinamide | |
| Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
| clofazimine | Not assoc w R | |||||
| pncA | 2290062 | c.-821G>A | upstream_gene_variant | 1.0 | pyrazinamide | |
| kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
| ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
| ald | 3087184 | c.368_373delCCGACG | disruptive_inframe_deletion | 1.0 | cycloserine | |
| Rv3083 | 3449452 | p.Val317Met | missense_variant | 1.0 | ethionamide | |
| lpqB | 3624350 | c.561G>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Not assoc w R - Interim | |||||
| lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
| bedaquiline | Uncertain significance | |||||
| mtrB | 3627302 | c.-689G>A | upstream_gene_variant | 1.0 | rifampicin | |
| bedaquiline | ||||||
| alr | 3840241 | p.Pro394Ser | missense_variant | 1.0 | cycloserine | |
| alr | 3840932 | c.489C>T | synonymous_variant | 1.0 | cycloserine | |
| ddn | 3986987 | c.144G>T | synonymous_variant | 1.0 | pretomanid | |
| delamanid | Not assoc w R - Interim | |||||
| ddn | 3987180 | p.Asp113Asn | missense_variant | 1.0 | pretomanid | |
| delamanid | Uncertain significance | |||||
| clpC1 | 4040824 | c.-120C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
| glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | levofloxacin | Not assoc w R |
| moxifloxacin | Not assoc w R | |||||
| isoniazid | Not assoc w R | |||||
| streptomycin | Not assoc w R | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Not assoc w R | |||||
| glpK | 4139131 | p.Glu209Lys | missense_variant | 1.0 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Not assoc w R | |||||
| ethambutol | Uncertain significance | |||||
| glpK | 4139183 | c.572dupG | frameshift_variant | 0.94 | levofloxacin | Uncertain significance |
| moxifloxacin | Uncertain significance | |||||
| isoniazid | Uncertain significance | |||||
| streptomycin | Uncertain significance | |||||
| rifampicin | Uncertain significance | |||||
| ethambutol | Uncertain significance | |||||
| embC | 4239843 | c.-20A>C | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| embA | 4244635 | p.Val468Ala | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embA | 4245147 | p.Pro639Ser | missense_variant | 1.0 | ethambutol | Not assoc w R - Interim |
| embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
| embB | 4247933 | p.Gly474Ser | missense_variant | 1.0 | ethambutol | |
| aftB | 4268735 | c.102C>G | synonymous_variant | 1.0 | ethambutol | |
| ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
| ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
| ethA | 4326928 | c.546C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
| ethA | 4327103 | p.Gly124Asp | missense_variant | 1.0 | ethionamide | Uncertain significance |
| whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
| capreomycin | Not assoc w R | |||||
| amikacin | Not assoc w R | |||||
| whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
| capreomycin | ||||||
| amikacin | ||||||
| gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
